Some questions regarding board design

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You're probably far better off (in cost and in eventual satisfaction) the less you depend on manipulation of your files by the board house.

It's possible to use tools like ViewMate

My vendor says just to label them "NONPTH" on the drill chart. You don't need a pad.

Yes.

Yes it is normally a negative. Not sure about clearance - ask them. Mine seem to increase the clearances themselves...

I usually do it as part of the drill chart, just a thin line whose center represents the edge of the board. I used to ask them what router they use and carefully draw in a channel that wide, but don't bother now. They seem to figure it all out themselves. You should ask them though. They may need to leave little bits that keep the circle attached to the rectangular panel.

Guess so, never tried asking for countersinking.

The Chinese vendor I use does each job separately, so it is no problem. Some of the lower cost European and US services may offer low prototype prices because they can combine your job as part of a larger panel. They therefore have stricter rules about what you can and cannot do while remaining in the low-cost scheme.

No pad required. Note in the Drill Drawing which holes are non-plated. I assume they drill after the final plating process is done. We supply a separate drill file for NPTH, but that isn't necessary.

Ask your vendor. They should have the capability to merge layers, even flip a negative, then merge with positive. I've done this in the early days using PCAD.

Ask your vendor. A good vendor can hold 2 mil clearance. Don't use zero or you will get mask on your pads. The clearance is for registration issues.

You can show this in the Drill Drawing. Show the board outline and dimensions. Complicated outlines, I include a drawing of the outline showing all the dimensions. Some places will route along an outline you provide on one of the layers, good board houses will go off a drawing. Shear cross-hairs aren't necessary. The board house will use their own targets and drill holes to align the stackup. The final board is routed out of the panel, not sheared.

Ask you vendor if they can do this. Put that in the drill drawing or a separate mechanical drawing. Also, note it verbally in your readme file that explains each layer name and how you want those layers processed (copper weight, layer separation, material, special features, layer merging, ...). We have a blind drill hole in one of our boards thats done after the final lamination. They're pretty good at controlling the depth.

Bottom line, you need to talk to your vendor. If they are a quick-turn prototype house, much of what you want can't be done at cheap prices. You'll need to resort to their full service offering.